Rosetta High Resolution Protein Structure Refinement Protocol - Revision history

Jma at 20:45, 6 January 2010

2010-01-06T20:45:45Z

← Older revision		Revision as of 20:45, 6 January 2010
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	== '''Introduction''' ==		== '''Introduction''' ==

	[http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rosetta.php Rosetta] is a molecular modeling software package developed in the Baker Laboratory (U. of Washington) for the study and prediction of protein structures, and protein-DNA and protein-protein interactions.  This section describes how the program has been used for the unrestrained refinement of X-ray and NMR protein structures in the NESG~~ (Ref.~~ 1).		[http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rosetta.php Rosetta] is a molecular modeling software package developed in the Baker Laboratory (U. of Washington) for the study and prediction of protein structures, and protein-DNA and protein-protein interactions.  This section describes how the program has been used for the unrestrained refinement of X-ray and NMR protein structures in the NESG [1].

	== '''Protocol''' ==		== '''Protocol''' ==
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	#Relax single input structure with backbone perturbations and sidechain repacking.		#Relax single input structure with backbone perturbations and sidechain repacking.

			<br>

	=== '''NMR Structure Refinement''' ===		=== '''NMR Structure Refinement''' ===
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	#Rebuild loops, relax and minimize		#Rebuild loops, relax and minimize

	=== '''Commands''' ===		=== '''Commands''' ===
	<pre>1. rosetta -score -fa_input -s xxxx.pdb -nstruct n -use_pdb_numbering		<pre>1. rosetta -score -fa_input -s xxxx.pdb -nstruct n -use_pdb_numbering
	2. rosetta aa 1pdb _ -relax -looprlx -s <your input file > -fa_input -loop_file <loop_file_name> -nstruct1		2. rosetta aa 1pdb _ -relax -looprlx -s <your input file > -fa_input -loop_file <loop_file_name> -nstruct1
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	=== '''Files for Download''' ===		=== '''Files for Download''' ===

	*Click to download [[~~media~~:~~Rosetta Protocol~~.doc\|Rosetta_Protocol.doc]]: Rosetta protocol in word format		*Click to download [[Media:Rosetta_Protocol.doc\|Rosetta_Protocol.doc]]: Rosetta protocol in word format
	*Click to download [[~~media~~:~~example NMR rosetta refinement~~.tar.gz\|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement		*Click to download [[Media:Example_NMR_rosetta_refinement.tar.gz\|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement
	*Click to download [[~~media~~:~~example Xray rosetta refinement~~.tar.gz\|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement		*Click to download [[Media:Example_Xray_rosetta_refinement.tar.gz\|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement

	<br>		<br>

	== '''References''' ==		== '''References''' ==

	1.  Ramelot, T.A., ~~Acton~~, T.B., Ma, L-C., ~~Xiao~~, R., Montelione, G.T. and Kennedy, M.A. (2008) Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.''PROTEINS 75'': 147 - 167.		[http://www.ncbi.nlm.nih.gov/pubmed/18816799?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1 1.  Ramelot, T.A., Raman, S., Kuzin, A.P., Xiao, R., Ma, L-C., Acton, T.B., Hunt, J.F., Montelione, G.T., Baker, D., and Kennedy, M.A. (2008) Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.''PROTEINS 75'': 147 - 167.]

	~~<br>~~

	~~<br>~~

	~~-- TheresaRamelot - 26 Aug 2008~~

	~~-- Edited by JimAramini - Nov 2009~~

Jma at 23:46, 5 November 2009

2009-11-05T23:46:54Z

← Older revision		Revision as of 23:46, 5 November 2009
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	#Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)		#Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)
	#Idealize geometry		#Idealize geometry
	#		#Rebuild loops, relax and minimize



	=== '''Commands''' ===		=== '''Commands''' ===

Jma at 23:43, 5 November 2009

2009-11-05T23:43:28Z

← Older revision		Revision as of 23:43, 5 November 2009
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	1.  Ramelot, T.A., Acton, T.B., Ma, L-C., Xiao, R., Montelione, G.T. and Kennedy, M.A. (2008) Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.''PROTEINS 75'': 147 - 167.		1.  Ramelot, T.A., Acton, T.B., Ma, L-C., Xiao, R., Montelione, G.T. and Kennedy, M.A. (2008) Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.''PROTEINS 75'': 147 - 167.

			<br>

			<br>

			-- TheresaRamelot - 26 Aug 2008

	-- TheresaRamelot - 26 Aug ~~2009~~

	-- Edited by JimAramini - Nov 2009		-- Edited by JimAramini - Nov 2009

Jma at 23:16, 5 November 2009

2009-11-05T23:16:01Z

← Older revision		Revision as of 23:16, 5 November 2009
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	=== '''Files for Download''' ===		=== '''Files for Download''' ===

	*Click to download [[~~NESG~~:~~%ATTACHURL%/~~Rosetta Protocol.doc\|Rosetta_Protocol.doc]]: Rosetta protocol in word format		*Click to download [[media:Rosetta Protocol.doc\|Rosetta_Protocol.doc]]: Rosetta protocol in word format
	*Click to download [[~~NESG~~:~~%ATTACHURL%/~~example NMR rosetta refinement.tar.gz\|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement		*Click to download [[media:example NMR rosetta refinement.tar.gz\|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement
	*Click to download [[~~NESG~~:~~%ATTACHURL%/~~example Xray rosetta refinement.tar.gz\|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement		*Click to download [[media:example Xray rosetta refinement.tar.gz\|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement

	<br>		<br>

	== '''References''' ==		== '''References''' ==

Jma at 23:14, 5 November 2009

2009-11-05T23:14:31Z

← Older revision		Revision as of 23:14, 5 November 2009
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	== '''References''' ==		== '''References''' ==

	1.  Ramelot, T.A., Acton, T.B., Ma, L-C., Xiao, R., Montelione, G.T. and Kennedy, M.A. (2008) Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.''PROTEINS 75'': 147 - 167.		1.  Ramelot, T.A., Acton, T.B., Ma, L-C., Xiao, R., Montelione, G.T. and Kennedy, M.A. (2008) Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.''PROTEINS 75'': 147 - 167.





			-- TheresaRamelot - 26 Aug 2009

			-- Edited by JimAramini - Nov 2009

Jma at 23:13, 5 November 2009

2009-11-05T23:13:36Z

← Older revision		Revision as of 23:13, 5 November 2009
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	*Click to download [[NESG:%ATTACHURL%/example NMR rosetta refinement.tar.gz\|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement		*Click to download [[NESG:%ATTACHURL%/example NMR rosetta refinement.tar.gz\|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement
	*Click to download [[NESG:%ATTACHURL%/example Xray rosetta refinement.tar.gz\|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement		*Click to download [[NESG:%ATTACHURL%/example Xray rosetta refinement.tar.gz\|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement

			<br>

			== '''References''' ==

			1.  Ramelot, T.A., Acton, T.B., Ma, L-C., Xiao, R., Montelione, G.T. and Kennedy, M.A. (2008) Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.''PROTEINS 75'': 147 - 167.

Jma at 23:09, 5 November 2009

2009-11-05T23:09:47Z

← Older revision		Revision as of 23:09, 5 November 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	[http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rosetta.php Rosetta] is a molecular modeling software package developed in the Baker Laboratory (U. of Washington) for the study and prediction of protein structures, and protein-DNA and protein-protein interactions.		[http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rosetta.php Rosetta] is a molecular modeling software package developed in the Baker Laboratory (U. of Washington) for the study and prediction of protein structures, and protein-DNA and protein-protein interactions.  This section describes how the program has been used for the unrestrained refinement of X-ray and NMR protein structures in the NESG (Ref. 1).

	== '''Protocol''' ==		== '''Protocol''' ==

Jma at 23:07, 5 November 2009

2009-11-05T23:07:51Z

← Older revision		Revision as of 23:07, 5 November 2009
Line 3:		Line 3:
	[http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rosetta.php Rosetta] is a molecular modeling software package developed in the Baker Laboratory (U. of Washington) for the study and prediction of protein structures, and protein-DNA and protein-protein interactions.		[http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rosetta.php Rosetta] is a molecular modeling software package developed in the Baker Laboratory (U. of Washington) for the study and prediction of protein structures, and protein-DNA and protein-protein interactions.

	== ~~'''~~'''Protocol'''~~'''~~ ==		== '''Protocol''' ==

	Before running Rosetta, please make directory with:		Before running Rosetta, please make directory with:
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	#Idealize geometry		#Idealize geometry
	#Relax single input structure with backbone perturbations and sidechain repacking.		#Relax single input structure with backbone perturbations and sidechain repacking.



	=== '''NMR Structure Refinement''' ===		=== '''NMR Structure Refinement''' ===
Line 30:		Line 32:
	#Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)		#Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)
	#Idealize geometry		#Idealize geometry
	#~~Rebuild loops, relax and minimize~~		#

	~~=== '''Commands''' ===~~

	~~<nowiki>~~
	~~# rosetta -score -fa_input -s xxxx.pdb -nstruct n -use_pdb_numbering~~
	~~# rosetta aa 1pdb _ -relax -looprlx -s <your input file > -fa_input -loop_file <loop_file_name> -nstruct1~~
	~~# rosetta -pose_idealize -s <input file name> -fa_input -nstruct 1~~
	# rosetta aa 1pdb _ -relax -farlx -looprlx -loop_file <loop_file_name> -ex1 -ex2 -fa_input -s <input pdb file> -random_loop -loop_skip_rate 0.3 -farlx_cycle_ratio 1.0 -full_filename -nstruct < number of structures you want>
	# rosetta aa 1pdb _ -relax -farlx -s <input pdb file> -fa_input -ex1 -ex2 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -full_filename -nstruct <as many structures as you want>
	~~</nowiki>~~

			=== '''Commands''' ===
			<pre>1. rosetta -score -fa_input -s xxxx.pdb -nstruct n -use_pdb_numbering
			2. rosetta aa 1pdb _ -relax -looprlx -s <your input file > -fa_input -loop_file <loop_file_name> -nstruct1
			3. rosetta -pose_idealize -s <input file name> -fa_input -nstruct 1
			4. rosetta aa 1pdb _ -relax -farlx -looprlx -loop_file <loop_file_name> -ex1 -ex2 -fa_input -s <input pdb file> -random_loop -loop_skip_rate 0.3 -farlx_cycle_ratio 1.0 -full_filename -nstruct < number of structures you want>
			5. rosetta aa 1pdb _ -relax -farlx -s <input pdb file> -fa_input -ex1 -ex2 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -full_filename -nstruct <as many structures as you want>
			</pre>
	=== '''Files for Download''' ===		=== '''Files for Download''' ===

Jma at 23:05, 5 November 2009

2009-11-05T23:05:45Z

← Older revision		Revision as of 23:05, 5 November 2009
Line 1:		Line 1:
	== '''~~Rosetta High Resolution Protein Structure Refinement Protocol~~''' ==		== '''Introduction''' ==

			[http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rosetta.php Rosetta] is a molecular modeling software package developed in the Baker Laboratory (U. of Washington) for the study and prediction of protein structures, and protein-DNA and protein-protein interactions.

	~~Before running Rosetta, please make directory with:~~		== ''''''Protocol'''''' ==
	* rosetta_database (directory)
	** paths.txt
	** 1pdb.pdb (PDB file for single xray or nmr structure, with chain A reference removed)
	** 1pdb_.fasta (containing full length sequence)
	** aa1pdb_03_05.200_v1_3 (3mer fragment files generated for 1pdb sequence)
	** aa1pdb_09_05.200_v1_3 (9mer fragment files generated for 1pdb sequence)
	~~Note: fragment files can be obtained from the [http://robetta.bakerlab.org/fragmentsubmit.jsp Robetta fragment server].~~

			Before running Rosetta, please make directory with:

	~~=== '''X-ray Structure Refinement''' ===~~		*rosetta_database (directory)
	~~# Input~~ pdb ~~files into Rosetta format~~		**paths.txt
	~~# Add "missing" residues, such as N- and C-term, relax~~		**1pdb.pdb (PDB file for single xray or nmr structure, with chain A reference removed)
	~~# Idealize geometry~~		**1pdb_.fasta (containing full length sequence)
	~~# Relax single input structure with backbone perturbations and sidechain repacking~~.		**aa1pdb_03_05.200_v1_3 (3mer fragment files generated for 1pdb sequence)
			**aa1pdb_09_05.200_v1_3 (9mer fragment files generated for 1pdb sequence)

	=== '''NMR Structure Refinement''' ===		Note: fragment files can be obtained from the [http://robetta.bakerlab.org/fragmentsubmit.jsp Robetta fragment server].

			<br>

			=== '''X-ray Structure Refinement''' ===

			#Input pdb files into Rosetta format
			#Add "missing" residues, such as N- and C-term, relax
			#Idealize geometry
			#Relax single input structure with backbone perturbations and sidechain repacking.

			=== '''NMR Structure Refinement''' ===

			#Input pdb files into Rosetta format
			#Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)
			#Idealize geometry
			#Rebuild loops, relax and minimize

			=== '''Commands''' ===

	~~# Input pdb files into Rosetta format~~
	~~# Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)~~
	~~# Idealize geometry~~
	~~# Rebuild loops, relax and minimize~~

	~~=== '''Commands''' ===~~
	<nowiki>		<nowiki>
	# rosetta -score -fa_input -s xxxx.pdb -nstruct n -use_pdb_numbering		# rosetta -score -fa_input -s xxxx.pdb -nstruct n -use_pdb_numbering
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	</nowiki>		</nowiki>

	=== '''Files for Download''' ===		=== '''Files for Download''' ===
	* Click to download [[NESG:%ATTACHURL%/~~Rosetta_Protocol~~.doc\|Rosetta_Protocol.doc]]: Rosetta protocol in word format
	* Click to download [[NESG:%ATTACHURL%/~~example_NMR_rosetta_refinement~~.tar.gz\|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement		*Click to download [[NESG:%ATTACHURL%/Rosetta Protocol.doc\|Rosetta_Protocol.doc]]: Rosetta protocol in word format
	* Click to download [[NESG:%ATTACHURL%/~~example_Xray_rosetta_refinement~~.tar.gz\|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement		*Click to download [[NESG:%ATTACHURL%/example NMR rosetta refinement.tar.gz\|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement
			*Click to download [[NESG:%ATTACHURL%/example Xray rosetta refinement.tar.gz\|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement

Jma: moved NESG:RosettaRefinement to Rosetta High Resolution Protein Structure Refinement Protocol

2009-11-05T22:59:16Z

moved NESG:RosettaRefinement to Rosetta High Resolution Protein Structure Refinement Protocol

← Older revision	Revision as of 22:59, 5 November 2009
(No difference)